11-32500461-T-C

Variant names:

• chr11-32500461-T-C
• rs10767942
• ENST00000690579.2:n.778T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000690579.2(WT1-AS):​n.778T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,136 control chromosomes in the GnomAD database, including 5,635 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (5635 hom., cov: 33)
• Consequence: WT1-AS ENST00000690579.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.834
• Publications: 13 publications found

Genes affected

WT1-AS (HGNC:18135): (WT1 antisense RNA) This gene is located upstream of the Wilms tumor 1 (WT1) gene; these two genes are bi-directionally transcribed from the same promoter region. This gene is imprinted in kidney, with preferential expression from the paternal allele. Imprinting defects at chromosome 11p13 may contribute to tumorigenesis. [provided by RefSeq, May 2014]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WT1-AS	ENST00000690579.2	n.778T>C		non_coding_transcript_exon_variant	Exon 2 of 2
WT1-AS	ENST00000813621.1	n.795T>C		non_coding_transcript_exon_variant	Exon 2 of 2
WT1-AS	ENST00000813622.1	n.871T>C		non_coding_transcript_exon_variant	Exon 3 of 3
WT1-AS	ENST00000813623.1	n.876T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38645 AN: 152018 Hom.: 5624 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.242

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.254 AC: 38672 AN: 152136 Hom.: 5635 Cov.: 33 AF XY: 0.257 AC XY: 19145 AN XY: 74380

African (AFR) AF: 0.305 AC: 12640 AN: 41504

American (AMR) AF: 0.322 AC: 4918 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3472

East Asian (EAS) AF: 0.659 AC: 3390 AN: 5148

South Asian (SAS) AF: 0.261 AC: 1257 AN: 4820

European-Finnish (FIN) AF: 0.193 AC: 2051 AN: 10604

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13196 AN: 67996

Other (OTH) AF: 0.245 AC: 518 AN: 2112

Alfa AF: 0.224 Hom.: 9571

Bravo AF: 0.270

Asia WGS AF: 0.447 AC: 1553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.42
DANN	Benign	0.45
PhyloP100		-0.83

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10767942; hg19: chr11-32522007;